According to the chart, the airplane climbed from 1,425' to 2,300' in only 12 seconds. That works out to 4,375 fpm during that segment. Since that kind of climb rate would obviously not be in the profile at that altitude and configuration (the aircraft should be shallowing it's climb rate in order to accelerate), and a premature flap retraction would not generate an increased climb rate, I gotta believe the pilots over controlled the pitch either through inattention or lack of finesse, which resulted in the airspeed decrease, altitude surge, and corresponding stall warning.
Or possibly but less likely, a computer malfunction. But if a computer did that, and they knew it, they would be fools for continuing the flight with a known computer issue.